how to stop the annoying, " Android is starting optimising app" on 5.1.1

[AC Question]

I have just rooted an Asus Nexus 7 ( grouper) and every time I start again, after powering off, I get the annoying "Android is starting."........Optimising app etc. Clearing cache, updating the apps, remove apps update did not clear this issue.
And what is worse is that the camera is either uninstalled, or, I have to remove the updates to show up on the welcoming screen.